Project Tic-Toc is a top-secret U.S. government effort to build an experimental time machine, known as "The Time Tunnel" due to its appearance as an elliptical passageway. The base for Project Tic-Toc is a huge, hidden underground complex in Arizona, 800 floors deep and employing more than 12,000 specialized personnel.^[1] The directors of the project are Dr. Douglas Phillips (Colbert), Dr. Anthony Newman (Darren), and Lt. General Heywood Kirk (Whit Bissell). The specialists assisting them are Dr. Raymond Swain (John Zaremba), a foremost expert in electronics, and Dr. Ann MacGregor (Lee Meriwether), an electrobiologist supervising the unit that determines how much force and heat a time traveler is able to withstand. The series is set in 1968, two years into the future from the actual broadcast season, 1966–1967.

Project Tic-Toc is in its 10th year when United States Senator Leroy Clark (Gary Merrill) comes to investigate to determine whether the project, which has cost $7.5 billion (equivalent to $68 billion in 2024), is worth continuing. Senator Clark feels the project is a waste of government funds. When speaking to Phillips, Kirk, and Newman in front of the Time Tunnel, he delivers an ultimatum – either they send someone into time and return him during the course of his visit or their funding will cease. Tony volunteers for this endeavor, but he is turned down by project director Doug Phillips. Defying this decision, Tony sends himself into time. Doug follows shortly after to rescue him, but they both continue to be lost in time. Senator Clark returns to Washington with the promise that funding will not be cut off to the project, leaving General Kirk in charge.

The stage is set for the progress of the series as Tony and Doug are now "switched" from one period in history to another, allowing episodes to be set in the past and future. Episodes two through 23 begin with the following narration (voiced by Dick Tufeld):

Two American scientists are lost in the swirling maze of past and future ages, during the first experiments on America's greatest and most secret project, the Time Tunnel. Tony Newman and Doug Phillips now tumble helplessly toward a new fantastic adventure, somewhere along the infinite corridors of time.

Tony and Doug become participants in past events such as the sinking of the Titanic, the attack on Pearl Harbor, the eruption of Krakatoa, Custer's Last Stand, and the Battle of the Alamo, among others. General Kirk, Ray, and Ann in the control room are able to locate them in time and space, observe them, occasionally communicate with them through voice contact, and send help. The series was abruptly cancelled in the summer of 1967 by ABC, before they were able to film the episode in which Tony and Doug are safely returned to the Time Tunnel complex.